Hello, I am using the Allen Cell Segmenter via napari, and am unable to use the workflows which incorporate the Watershed function (from scikit-image). This results in a failure of the workflow to segment the given image in the workflow and batch applications. I get the following error message when running these work flows:
****A napari user on stackflow had the following comment:
watershed was moved from skimage.morphology to skimage.segmentation in version 0.17. There was a pointer from morphology to the new function in segmentation in 0.17 and 0.18, but it was removed in 0.19. The Allen Cell Segmenter needs to be updated to match the more modern scikit-image version, so I would raise an issue in their GitHub repository if I were you.****
Downgrading to scikit-image 0.18 could fix the Allen Cell Segmenter itself, but unfortunately napari requires 0.19+.
Error message
ImportError: cannot import name 'watershed' from 'skimage.morphology' (C:\Users\Murryadmin\anaconda3\envs\napari-env\lib\site-packages\skimage\morphologyinit.py)
c:\users\murryadmin\anaconda3\envs\napari-env\lib\site-packages\aicssegmentation\core\utils.py(449)watershed_wrapper() -> from skimage.morphology import watershed, dilation, ball
Expected Behavior
Watershed function should be imported and final segmented image should be produced.
Reproduction
Please list the exact steps we can take to reproduce this bug.
Run workflow which has watershed function (e.g., the cetn2 pipeline).
"Run all" command/button on pipeline
Error occurs
Environment
Operating system: Windows 10, 64 bit
Python version: Python 3.9.13
napari version: 0.4.16
How did you install the napari viewer: pip install
Description
Hello, I am using the Allen Cell Segmenter via napari, and am unable to use the workflows which incorporate the Watershed function (from scikit-image). This results in a failure of the workflow to segment the given image in the workflow and batch applications. I get the following error message when running these work flows:
****A napari user on stackflow had the following comment:
watershed was moved from skimage.morphology to skimage.segmentation in version 0.17. There was a pointer from morphology to the new function in segmentation in 0.17 and 0.18, but it was removed in 0.19. The Allen Cell Segmenter needs to be updated to match the more modern scikit-image version, so I would raise an issue in their GitHub repository if I were you.****
Downgrading to scikit-image 0.18 could fix the Allen Cell Segmenter itself, but unfortunately napari requires 0.19+.
Error message
ImportError: cannot import name 'watershed' from 'skimage.morphology' (C:\Users\Murryadmin\anaconda3\envs\napari-env\lib\site-packages\skimage\morphologyinit.py)
c:\users\murryadmin\anaconda3\envs\napari-env\lib\site-packages\aicssegmentation\core\utils.py(449)watershed_wrapper() -> from skimage.morphology import watershed, dilation, ball
Expected Behavior
Watershed function should be imported and final segmented image should be produced.
Reproduction
Please list the exact steps we can take to reproduce this bug.
Environment